☰ Navigation Tabs
Fragments bound to the OXA-48 beta-lactamase: Compound 17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1M HEPES pH 7.5, 8-12% PEG8000, 4% butanol
Crystal Properties Matthews coefficient Solvent content 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.523 α = 90 b = 124.31 β = 98.263 c = 108.742 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.478 49.38 98.02 0.08237 9.67 3.3 195258 16.0316230801
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.478 1.531 85.02 1.033 0.82 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3HBR 1.60000241571 49.3793661959 1.35792690821 156895 1687 99.7799556095 0.145862928729 0.145573684921 0.1471 0.172474668469 0.1746 Random selection 26.0672524111
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.5010754664 f_angle_d 0.949369669528 f_chiral_restr 0.0579356964116 f_bond_d 0.00844393936441 f_plane_restr 0.00651653492992
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7944 Nucleic Acid Atoms Solvent Atoms 1279 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing XDS data scaling